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GiA Roots: software for the high throughput analysis of plant root system architecture.

Galkovskyi T, Mileyko Y, Bucksch A, Moore B, Symonova O, Price CA, Topp CN, Iyer-Pascuzzi AS, Zurek PR, Fang S, Harer J, Benfey PN, Weitz JS.

BMC Plant Biol. 2012 Jul 26;12:116. doi: 10.1186/1471-2229-12-116.


Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems.

Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao Y, Belcher H, Harer J, Weitz JS, Benfey PN.

Plant Physiol. 2010 Mar;152(3):1148-57. doi: 10.1104/pp.109.150748. Epub 2010 Jan 27.


Three-dimensional root phenotyping with a novel imaging and software platform.

Clark RT, MacCurdy RB, Jung JK, Shaff JE, McCouch SR, Aneshansley DJ, Kochian LV.

Plant Physiol. 2011 Jun;156(2):455-65. doi: 10.1104/pp.110.169102. Epub 2011 Mar 31.


RootNav: navigating images of complex root architectures.

Pound MP, French AP, Atkinson JA, Wells DM, Bennett MJ, Pridmore T.

Plant Physiol. 2013 Aug;162(4):1802-14. doi: 10.1104/pp.113.221531. Epub 2013 Jun 13.


3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture.

Topp CN, Iyer-Pascuzzi AS, Anderson JT, Lee CR, Zurek PR, Symonova O, Zheng Y, Bucksch A, Mileyko Y, Galkovskyi T, Moore BT, Harer J, Edelsbrunner H, Mitchell-Olds T, Weitz JS, Benfey PN.

Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):E1695-704. doi: 10.1073/pnas.1304354110. Epub 2013 Apr 11.


High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability.

Ingram PA, Zhu J, Shariff A, Davis IW, Benfey PN, Elich T.

Philos Trans R Soc Lond B Biol Sci. 2012 Jun 5;367(1595):1559-69. doi: 10.1098/rstb.2011.0241.


EZ-Rhizo: integrated software for the fast and accurate measurement of root system architecture.

Armengaud P, Zambaux K, Hills A, Sulpice R, Pattison RJ, Blatt MR, Amtmann A.

Plant J. 2009 Mar;57(5):945-56. doi: 10.1111/j.1365-313X.2008.03739.x. Epub 2008 Nov 4.


RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.

Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM.

Plant Physiol. 2013 Mar;161(3):1086-96. doi: 10.1104/pp.112.210872. Epub 2013 Jan 18.


From lab to field, new approaches to phenotyping root system architecture.

Zhu J, Ingram PA, Benfey PN, Elich T.

Curr Opin Plant Biol. 2011 Jun;14(3):310-7. doi: 10.1016/j.pbi.2011.03.020. Epub 2011 Apr 27.


High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development.

Clark RT, Famoso AN, Zhao K, Shaff JE, Craft EJ, Bustamante CD, McCouch SR, Aneshansley DJ, Kochian LV.

Plant Cell Environ. 2013 Feb;36(2):454-66. doi: 10.1111/j.1365-3040.2012.02587.x. Epub 2012 Sep 3.


High-throughput feature counting and measurement of roots.

Naeem A, French AP, Wells DM, Pridmore TP.

Bioinformatics. 2011 May 1;27(9):1337-8. doi: 10.1093/bioinformatics/btr126. Epub 2011 Mar 12.


P-TRAP: a Panicle TRAit Phenotyping tool.

A L-Tam F, Adam H, Anjos Ad, Lorieux M, Larmande P, Ghesquière A, Jouannic S, Shahbazkia HR.

BMC Plant Biol. 2013 Aug 29;13:122. doi: 10.1186/1471-2229-13-122.


Comparing simple root phenotyping methods on a core set of rice genotypes.

Shrestha R, Al-Shugeairy Z, Al-Ogaidi F, Munasinghe M, Radermacher M, Vandenhirtz J, Price AH.

Plant Biol (Stuttg). 2014 May;16(3):632-42. doi: 10.1111/plb.12096. Epub 2013 Sep 9.


Analysis of maize (Zea mays L.) seedling roots with the high-throughput image analysis tool ARIA (Automatic Root Image Analysis).

Pace J, Lee N, Naik HS, Ganapathysubramanian B, Lübberstedt T.

PLoS One. 2014 Sep 24;9(9):e108255. doi: 10.1371/journal.pone.0108255. eCollection 2014.


Recovering the dynamics of root growth and development using novel image acquisition and analysis methods.

Wells DM, French AP, Naeem A, Ishaq O, Traini R, Hijazi HI, Bennett MJ, Pridmore TP.

Philos Trans R Soc Lond B Biol Sci. 2012 Jun 5;367(1595):1517-24. doi: 10.1098/rstb.2011.0291. Erratum in: Philos Trans R Soc Lond B Biol Sci. 2012 Aug 5;367(1599):2245. Hijazi, Hussein [corrected to Hijazi, Hussein I].


Recovering root system traits using image analysis exemplified by two-dimensional neutron radiography images of lupine.

Leitner D, Felderer B, Vontobel P, Schnepf A.

Plant Physiol. 2014 Jan;164(1):24-35. doi: 10.1104/pp.113.227892. Epub 2013 Nov 11.


Genotypic recognition and spatial responses by rice roots.

Fang S, Clark RT, Zheng Y, Iyer-Pascuzzi AS, Weitz JS, Kochian LV, Edelsbrunner H, Liao H, Benfey PN.

Proc Natl Acad Sci U S A. 2013 Feb 12;110(7):2670-5. doi: 10.1073/pnas.1222821110. Epub 2013 Jan 29.


A scanner system for high-resolution quantification of variation in root growth dynamics of Brassica rapa genotypes.

Adu MO, Chatot A, Wiesel L, Bennett MJ, Broadley MR, White PJ, Dupuy LX.

J Exp Bot. 2014 May;65(8):2039-48. doi: 10.1093/jxb/eru048. Epub 2014 Mar 6.


A complete system for 3D reconstruction of roots for phenotypic analysis.

Kumar P, Cai J, Miklavcic SJ.

Adv Exp Med Biol. 2015;823:249-70. doi: 10.1007/978-3-319-10984-8_14.


A novel image-analysis toolbox enabling quantitative analysis of root system architecture.

Lobet G, Pagès L, Draye X.

Plant Physiol. 2011 Sep;157(1):29-39. doi: 10.1104/pp.111.179895. Epub 2011 Jul 19.

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